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Zhang SM, Paulin CB, Shu H, Yagüe-Capilla M, Michel M, Marttila P, Ortis F, Bwanika HC, Dirks C, Venkatram RP, Wiita E, Jemth AS, Almlöf I, Loseva O, Hormann FM, Koolmeister T, Linde E, Lee S, Llona-Minguez S, Haraldsson M, Axelsson H, Strömberg K, Homan EJ, Scobie M, Lundbäck T, Helleday T, Rudd SG. Identification and evaluation of small-molecule inhibitors against the dNTPase SAMHD1 via a comprehensive screening funnel. iScience 2024; 27:108907. [PMID: 38318365 PMCID: PMC10839966 DOI: 10.1016/j.isci.2024.108907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 09/05/2023] [Accepted: 01/10/2024] [Indexed: 02/07/2024] Open
Abstract
SAMHD1 is a dNTP triphosphohydrolase governing nucleotide pool homeostasis and can detoxify chemotherapy metabolites controlling their clinical responses. To understand SAMHD1 biology and investigate the potential of targeting SAMHD1 as neoadjuvant to current chemotherapies, we set out to discover selective small-molecule inhibitors. Here, we report a discovery pipeline encompassing a biochemical screening campaign and a set of complementary biochemical, biophysical, and cell-based readouts for rigorous characterization of the screen output. The identified small molecules, TH6342 and analogs, accompanied by inactive control TH7126, demonstrated specific, low μM potency against both physiological and oncology-drug-derived substrates. By coupling kinetic studies with thermal shift assays, we reveal the inhibitory mechanism of TH6342 and analogs, which engage pre-tetrameric SAMHD1 and deter oligomerization and allosteric activation without occupying nucleotide-binding pockets. Altogether, our study diversifies inhibitory modes against SAMHD1, and the discovery pipeline reported herein represents a thorough framework for future SAMHD1 inhibitor development.
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Affiliation(s)
- Si Min Zhang
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Cynthia B.J. Paulin
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Huazhang Shu
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Miriam Yagüe-Capilla
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Maurice Michel
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Petra Marttila
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Florian Ortis
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Henri Colyn Bwanika
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Christopher Dirks
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Rajagopal Papagudi Venkatram
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Elisée Wiita
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Ann-Sofie Jemth
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Ingrid Almlöf
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Olga Loseva
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Femke M. Hormann
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Tobias Koolmeister
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Erika Linde
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Sun Lee
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Sabin Llona-Minguez
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Martin Haraldsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory (SciLifeLab), Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Hanna Axelsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory (SciLifeLab), Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Kia Strömberg
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Evert J. Homan
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Martin Scobie
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden, Science for Life Laboratory (SciLifeLab), Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 65 Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
- Weston Park Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK
| | - Sean G. Rudd
- Science for Life Laboratory (SciLifeLab), Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden
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Huang Q, Tan C, Zheng C, Meng H, Wang Z, Lin GQ, Zhang W, Chen B, He QL. DCTPP1, a reliable Q-biomarker for comprehensive evaluation of the quality of tripterygium glycoside tablets based on chemical references. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 119:154972. [PMID: 37531903 DOI: 10.1016/j.phymed.2023.154972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/14/2023] [Accepted: 07/15/2023] [Indexed: 08/04/2023]
Abstract
BACKGROUND As first-line clinical drugs, tripterygium glycoside tablets (TGTs) often have inconsistent efficacy and toxic side effects, mainly due to inadequate quality control. Therefore, clinically relevant quality standards for TGTs are urgently required. PURPOSE Based on chemical substances and considering pharmacological efficacy, we aimed to develop an effective quality evaluation method for TGTs. METHODS Representative commercial samples of TGTs were collected from different manufacturers, and qualitative UHPLC/LTQ-Orbitrap-MS and quantitative UHPLC-MS/MS analysis methods were successfully applied to evaluate their quality similarities and differences based on their chemical properties. Then the anti-immunity, anti-inflammatory and antitumor activities of TGTs and related monomers were evaluated using Jurkat, RAW264.7, MIA PaCa-2, and PANC-1 as cellular models. Subsequently, we predicted and verified small molecule-DCTPP1 interactions via molecular docking using the established DCTPP1 enzymatic activity assay. Finally, we performed a gray relational analysis to evaluate the chemical characteristics and biological effects of TGTs produced by different manufacturers. RESULTS We collected 24 batches of TGTs (D01-D24) from 5 manufacturers (Co. A, Co. B, Co. C, Co. D, Co. E) for quality evaluation. The chemical composition analysis revealed significant differences in the substance bases of the samples. The D02, D18-D20 samples from Co. B constituted a separate group that differed from other samples, mainly in their absence of diterpenoids and triterpenoids, including triptolide, triptophenolide, and triptonide. In vitro anti-immunity, antitumor and anti-inflammatory tests using the same TGT concentration revealed that, except for D02, D18-D20, the remaining 20 samples exhibited different degrees of anti-immunity, antitumor and anti-inflammatory activity. Our experiments verified that triptolide, triptophenolide, and triptonide were all DCTPP1 inhibitors, and that TGTs generally exhibited DCTPP1 enzyme inhibitory activity. Moreover, the inhibitory activity of D02, D18-D20 samples from Co. B was much lower than that of the other samples, with a nearly tenfold difference in IC50. Further comprehensive analysis revealed a high correlation between DCTPP1 enzyme inhibition activity and the anti-immunity and antitumor and anti-inflammatory activities of these samples. CONCLUSION The established DCTPP1 enzymatic activity assay proved suitable for quantitative pharmacological and pharmaceutical analysis to complement the existing quality control system for TGTs and to evaluate their effectiveness.
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Affiliation(s)
- QinWei Huang
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - ChunMei Tan
- NMPA Key Laboratory for Quality Evaluation of Traditional Chinese Medicine (Traditional Chinese Patent Medicine), Zhejiang Institute for Food and Drug Control, Hangzhou 310052, China
| | - Cheng Zheng
- NMPA Key Laboratory for Quality Evaluation of Traditional Chinese Medicine (Traditional Chinese Patent Medicine), Zhejiang Institute for Food and Drug Control, Hangzhou 310052, China
| | - Hong Meng
- NMPA Key Laboratory for Animal Alternative Testing Technology of Cosmetics, Zhejiang Institute for Food and Drug Control, Hangzhou 310052, China
| | - ZhengNan Wang
- NMPA Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Zhejiang Institute for Food and Drug Control, Hangzhou 310052, China
| | - Guo-Qiang Lin
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - WenTing Zhang
- NMPA Key Laboratory for Quality Evaluation of Traditional Chinese Medicine (Traditional Chinese Patent Medicine), Zhejiang Institute for Food and Drug Control, Hangzhou 310052, China.
| | - BiLian Chen
- NMPA Key Laboratory for Quality Evaluation of Traditional Chinese Medicine (Traditional Chinese Patent Medicine), Zhejiang Institute for Food and Drug Control, Hangzhou 310052, China.
| | - Qing-Li He
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine (IRI), Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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3
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Basantcev AV, Danilin AA, Golovanov AA, Purygin PP. Synthesis of 1-(4-Alkoxybenzyl)-1H-(benz)imidazoles. RUSS J GEN CHEM+ 2022. [DOI: 10.1134/s1070363222070167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Chen PJ, Kelly AM, Blair DJ, Burke MD. Preparation of MIDA Anhydride and Reaction with Boronic Acids. ORGANIC SYNTHESES; AN ANNUAL PUBLICATION OF SATISFACTORY METHODS FOR THE PREPARATION OF ORGANIC CHEMICALS 2022; 99:92-112. [PMID: 37587918 PMCID: PMC10428519 DOI: 10.15227/orgsyn.099.0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Affiliation(s)
- Peng-Jui Chen
- Roger Adams Laboratory, School of Chemical Sciences, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, IL 61801, USA
| | - Aidan M. Kelly
- Roger Adams Laboratory, School of Chemical Sciences, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, IL 61801, USA
| | - Daniel J. Blair
- Roger Adams Laboratory, School of Chemical Sciences, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, IL 61801, USA
| | - Martin D. Burke
- Roger Adams Laboratory, School of Chemical Sciences, University of Illinois at Urbana-Champaign, 600 S Mathews Avenue, Urbana, IL 61801, USA
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5
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Dai Y, Zhang X, Liu Y, Yu H, Su W, Zhou J, Ye Q, Huang Z. 1,6;2,3-Bis-BN Cyclohexane: Synthesis, Structure, and Hydrogen Release. J Am Chem Soc 2022; 144:8434-8438. [PMID: 35446021 DOI: 10.1021/jacs.1c13581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BN/CC isosterism has been widely investigated as a strategy to expand carbon-based compounds. The introduction of BN units in organic molecules always results in novel properties. In this work, we reported the first synthesis and characterization of 1,6;2,3-bis-BN cyclohexane, an isostere of cyclohexane with two adjacent BN pairs. Its ring flipping barrier is similar to that of cyclohexane. Protic hydrogens on N in 1,6;2,3-bis-BN cyclohexane show higher reactivity than its isomeric bis-BN cyclohexane. This compound exhibits an appealing hydrogen storage capability of >9.0 wt %, nearly twice as much as the 1,2;4,5-bis-BN cyclohexane.
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Affiliation(s)
- Yan Dai
- School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Xin Zhang
- State Key Laboratory of Silicon Materials and School of Materials Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Yongfeng Liu
- State Key Laboratory of Silicon Materials and School of Materials Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Haibo Yu
- Molecular Horizons and School of Chemistry & Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, New South Wales 2522, Australia
| | - Wei Su
- Department of Chemistry, Southern University of Science and Technology, 518055 Shenzhen, China
| | - John Zhou
- School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
| | - Qing Ye
- Department of Chemistry, Southern University of Science and Technology, 518055 Shenzhen, China.,Institut für Anorganische Chemie and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Zhenguo Huang
- School of Civil and Environmental Engineering, University of Technology Sydney, Sydney, New South Wales 2007, Australia
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6
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Song S, Gao P, Sun L, Kang D, Kongsted J, Poongavanam V, Zhan P, Liu X. Recent developments in the medicinal chemistry of single boron atom-containing compounds. Acta Pharm Sin B 2021; 11:3035-3059. [PMID: 34729302 PMCID: PMC8546671 DOI: 10.1016/j.apsb.2021.01.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/25/2020] [Accepted: 01/05/2021] [Indexed: 12/11/2022] Open
Abstract
Various boron-containing drugs have been approved for clinical use over the past two decades, and more are currently in clinical trials. The increasing interest in boron-containing compounds is due to their unique binding properties to biological targets; for example, boron substitution can be used to modulate biological activity, pharmacokinetic properties, and drug resistance. In this perspective, we aim to comprehensively review the current status of boron compounds in drug discovery, focusing especially on progress from 2015 to December 2020. We classify these compounds into groups showing anticancer, antibacterial, antiviral, antiparasitic and other activities, and discuss the biological targets associated with each activity, as well as potential future developments.
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Key Words
- ACTs, artemisinin combination therapies
- ADCs, Acinetobacter-derived cephalosporinases
- AML, acute myeloid leukemia
- AMT, aminopterin
- BLs, β-lactamases
- BNCT, boron neutron capture therapy
- BNNPs, boron nitride nanoparticles
- BNNTs, boron nitride nanotubes
- Boron-containing compounds
- CEs, carboxylesterases
- CIA, collagen-induced arthritis
- COVID-19, coronavirus disease 2019
- ClpP, casein protease P
- Covalent inhibitors
- GSH, glutathione
- HADC1, class I histone deacetylase
- HBV, hepatitis B virus
- HCV, hepatitis C virus
- HIV, human immunodeficiency virus
- LeuRS, leucyl-tRNA synthetase
- Linker components
- MBLs, metal β-lactamases
- MDR-TB, multidrug-resistant tuberculosis
- MERS, Middle East respiratory syndrome
- MIDA, N-methyliminodiacetic acid
- MM, multiple myeloma
- MTX, methotrexate
- Mcl-1, myeloid cell leukemia 1
- Mtb, Mycobacterium tuberculosis
- NA, neuraminidase
- NS5B, non-nucleoside polymerase
- OBORT, oxaborole tRNA capture
- OPs, organophosphate
- PBA, phenylboronic acid
- PDB, Protein Data Bank
- PPI, protein–protein interaction
- Prodrug
- QM, quinone methide
- RA, rheumatoid arthritis
- ROS, reactive oxygen species
- SARS-CoV-2, syndrome coronavirus 2
- SBLs, serine β-lactamases
- SERD, selective estrogen receptor downregulator
- SHA, salicyl hydroxamic acid
- SaClpP, Staphylococcus aureus caseinolytic protease P
- TB, tuberculosis
- TTR, transthyretin
- U4CR, Ugi 4-component reaction
- cUTI, complex urinary tract infection
- dCTPase, dCTPase pyrophosphatase
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Affiliation(s)
- Shu Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Ping Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Lin Sun
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M. DK-5230, Denmark
| | - Vasanthanathan Poongavanam
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M. DK-5230, Denmark
- Corresponding authors. Tel./fax: +86 531 88380270.
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
- Corresponding authors. Tel./fax: +86 531 88380270.
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Ji'nan 250012, China
- Corresponding authors. Tel./fax: +86 531 88380270.
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Yesudhas D, Srivastava A, Gromiha MM. COVID-19 outbreak: history, mechanism, transmission, structural studies and therapeutics. Infection 2021; 49:199-213. [PMID: 32886331 PMCID: PMC7472674 DOI: 10.1007/s15010-020-01516-2] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/25/2020] [Indexed: 01/08/2023]
Abstract
PURPOSE The coronavirus outbreak emerged as a severe pandemic, claiming more than 0.8 million lives across the world and raised a major global health concern. We survey the history and mechanism of coronaviruses, and the structural characteristics of the spike protein and its key residues responsible for human transmissions. METHODS We have carried out a systematic review to summarize the origin, transmission and etiology of COVID-19. The structural analysis of the spike protein and its disordered residues explains the mechanism of the viral transmission. A meta-data analysis of the therapeutic compounds targeting the SARS-CoV-2 is also included. RESULTS Coronaviruses can cross the species barrier and infect humans with unexpected consequences for public health. The transmission rate of SARS-CoV-2 infection is higher compared to that of the closely related SARS-CoV infections. In SARS-CoV-2 infection, intrinsically disordered regions are observed at the interface of the spike protein and ACE2 receptor, providing a shape complementarity to the complex. The key residues of the spike protein have stronger binding affinity with ACE2. These can be probable reasons for the higher transmission rate of SARS-CoV-2. In addition, we have also discussed the therapeutic compounds and the vaccines to target SARS-CoV-2, which can help researchers to develop effective drugs/vaccines for COVID-19. The overall history and mechanism of entry of SARS-CoV-2 along with structural study of spike-ACE2 complex provide insights to understand disease pathogenesis and development of vaccines and drugs.
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Affiliation(s)
- Dhanusha Yesudhas
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.
| | - Ambuj Srivastava
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India.
- School of Computing, Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan.
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8
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Vanda D, Canale V, Chaumont-Dubel S, Kurczab R, Satała G, Koczurkiewicz-Adamczyk P, Krawczyk M, Pietruś W, Blicharz K, Pękala E, Bojarski AJ, Popik P, Marin P, Soural M, Zajdel P. Imidazopyridine-Based 5-HT 6 Receptor Neutral Antagonists: Impact of N1-Benzyl and N1-Phenylsulfonyl Fragments on Different Receptor Conformational States. J Med Chem 2021; 64:1180-1196. [PMID: 33439019 DOI: 10.1021/acs.jmedchem.0c02009] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
G-protein coupled receptors (GPCRs) exist in an equilibrium of multiple conformational states, including different active states, which depend on the nature of the bound ligand. In consequence, different conformational states can initiate specific signal transduction pathways. The study identified compound 7e, which acts as a potent 5-hydroxytryptamine type 6 receptor (5-HT6R) neutral antagonist at Gs and does not impact neurite growth (process controlled by Cdk5). MD simulations highlighted receptor conformational changes for 7e and inverse agonist PZ-1444. In cell-based assays, neutral antagonists of the 5-HT6R (7e and CPPQ), but not inverse agonists (SB-258585, intepirdine, PZ-1444), displayed glioprotective properties against 6-hydroxydopamine-induced and doxorubicin-induced cytotoxicity. These suggest that targeting the activated conformational state of the 5-HT6R with neutral antagonists implicates the protecting properties of astrocytes. Additionally, 7e prevented scopolamine-induced learning deficits in the novel object recognition test in rats. We propose 7e as a probe for further understanding of the functional outcomes of different states of the 5-HT6R.
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Affiliation(s)
- David Vanda
- Faculty of Science, Department of Organic Chemistry, Palacký University, 17. listopadu 12, Olomouc 771 46, Czech Republic
| | - Vittorio Canale
- Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Street, Kraków 30-688, Poland
| | - Severine Chaumont-Dubel
- Institut de Génomique Fonctionnelle, Univ. Montpellier, INSERM, CNRS, 141 Rue de la Cardonille, Montpellier 34-094, France
| | - Rafał Kurczab
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, Kraków 31-343, Poland
| | - Grzegorz Satała
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, Kraków 31-343, Poland
| | | | - Martyna Krawczyk
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, Kraków 31-343, Poland
| | - Wojciech Pietruś
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, Kraków 31-343, Poland
| | - Klaudia Blicharz
- Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Street, Kraków 30-688, Poland
| | - Elżbieta Pękala
- Faculty of Pharmacy, Jagiellonian University Medical College, 9 Medyczna Street, Kraków 30-688, Poland
| | - Andrzej J Bojarski
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, Kraków 31-343, Poland
| | - Piotr Popik
- Maj Institute of Pharmacology, Polish Academy of Sciences, 12 Smętna Street, Kraków 31-343, Poland
| | - Philippe Marin
- Institut de Génomique Fonctionnelle, Univ. Montpellier, INSERM, CNRS, 141 Rue de la Cardonille, Montpellier 34-094, France
| | - Miroslav Soural
- Faculty of Science, Department of Organic Chemistry, Palacký University, 17. listopadu 12, Olomouc 771 46, Czech Republic.,Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Hněvotínská 5, Olomouc 779 00, Czech Republic
| | - Paweł Zajdel
- Faculty of Pharmacy, Department of Organic Chemistry, Jagiellonian University Medical College, 9 Medyczna Street, Kraków 30-688, Poland
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Tong L, Zhao Q, Datan E, Lin GQ, Minn I, Pomper MG, Yu B, Romo D, He QL, Liu JO. Triptolide: reflections on two decades of research and prospects for the future. Nat Prod Rep 2021; 38:843-860. [PMID: 33146205 DOI: 10.1039/d0np00054j] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: 2000 to 2020 Triptolide is a bioactive diterpene triepoxide isolated from Tripterygium wilfordii Hook F, a traditional Chinese medicinal plant whose extracts have been used as anti-inflammatory and immunosuppressive remedies for centuries. Although triptolide and its analogs exhibit potent bioactivities against various cancers, and inflammatory and autoimmune diseases, none of them has been approved to be used in the clinic. This review highlights advances in material sourcing, molecular mechanisms, clinical progress and new drug design strategies for triptolide over the past two decades, along with some prospects for the future course of development of triptolide.
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Affiliation(s)
- Lu Tong
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China.
| | - Qunfei Zhao
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China.
| | - Emmanuel Datan
- Department of Pharmacology, Johns Hopkins School of Medicine, 725 North Wolfe Street, Hunterian Building, Room 516, Baltimore, MD 21205, USA.
| | - Guo-Qiang Lin
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China. and CAS Key Laboratory of Synthetic Chemistry of Natural Substances, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Il Minn
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Martin G Pomper
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Biao Yu
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Daniel Romo
- Department of Chemistry and Biochemistry, The CPRIT Synthesis and Drug Lead Discovery Laboratory, Baylor University, Waco, Texas 76710, USA
| | - Qing-Li He
- The Research Center of Chiral Drugs, Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Shanghai 201203, China.
| | - Jun O Liu
- Department of Pharmacology, Johns Hopkins School of Medicine, 725 North Wolfe Street, Hunterian Building, Room 516, Baltimore, MD 21205, USA.
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10
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Kelly AM, Chen PJ, Klubnick J, Blair DJ, Burke MD. A Mild Method for Making MIDA Boronates. Org Lett 2020; 22:9408-9414. [DOI: 10.1021/acs.orglett.0c02449] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aidan M. Kelly
- Roger Adams Laboratory, School of Chemical Sciences, University of Illinois at Urbana−Champaign, 600 S, Mathews Avenue, Urbana, Illinois 61801, United States
| | - Peng-Jui Chen
- Roger Adams Laboratory, School of Chemical Sciences, University of Illinois at Urbana−Champaign, 600 S, Mathews Avenue, Urbana, Illinois 61801, United States
| | - Jenna Klubnick
- Roger Adams Laboratory, School of Chemical Sciences, University of Illinois at Urbana−Champaign, 600 S, Mathews Avenue, Urbana, Illinois 61801, United States
| | - Daniel J. Blair
- Roger Adams Laboratory, School of Chemical Sciences, University of Illinois at Urbana−Champaign, 600 S, Mathews Avenue, Urbana, Illinois 61801, United States
| | - Martin D. Burke
- Roger Adams Laboratory, School of Chemical Sciences, University of Illinois at Urbana−Champaign, 600 S, Mathews Avenue, Urbana, Illinois 61801, United States
- Carle Illinois College of Medicine, 807 South Wright Street, Urbana, Illinois 61820, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, 1206 West Gregory Dr., Urbana, Illinois 61801, United States
- Arnold and Mabel Beckman Institute, University of Illinois at Urbana−Champaign, 405 North Mathews Ave., Urbana, Illinois 61801, United States
- Department of Biochemistry, University of Illinois at Urbana−Champaign, 600 S Mathews Avenue, Urbana, Illinois 61801, United States
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11
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12
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Michel M, Homan EJ, Wiita E, Pedersen K, Almlöf I, Gustavsson AL, Lundbäck T, Helleday T, Warpman Berglund U. In silico Druggability Assessment of the NUDIX Hydrolase Protein Family as a Workflow for Target Prioritization. Front Chem 2020; 8:443. [PMID: 32548091 PMCID: PMC7274155 DOI: 10.3389/fchem.2020.00443] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 04/28/2020] [Indexed: 01/13/2023] Open
Abstract
Computational chemistry has now been widely accepted as a useful tool for shortening lead times in early drug discovery. When selecting new potential drug targets, it is important to assess the likelihood of finding suitable starting points for lead generation before pursuing costly high-throughput screening campaigns. By exploiting available high-resolution crystal structures, an in silico druggability assessment can facilitate the decision of whether, and in cases where several protein family members exist, which of these to pursue experimentally. Many of the algorithms and software suites commonly applied for in silico druggability assessment are complex, technically challenging and not always user-friendly. Here we applied the intuitive open access servers of DoGSite, FTMap and CryptoSite to comprehensively predict ligand binding pockets, druggability scores and conformationally active regions of the NUDIX protein family. In parallel we analyzed potential ligand binding sites, their druggability and pocket parameter using Schrödinger's SiteMap. Then an in silico docking cascade of a subset of the ZINC FragNow library using the Glide docking program was performed to assess identified pockets for large-scale small-molecule binding. Subsequently, this initial dual ranking of druggable sites within the NUDIX protein family was benchmarked against experimental hit rates obtained both in-house and by others from traditional biochemical and fragment screening campaigns. The observed correlation suggests that the presented user-friendly workflow of a dual parallel in silico druggability assessment is applicable as a standalone method for decision on target prioritization and exclusion in future screening campaigns.
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Affiliation(s)
- Maurice Michel
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Evert J Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Elisée Wiita
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Kia Pedersen
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Ingrid Almlöf
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Anna-Lena Gustavsson
- Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.,Department of Oncology and Metabolism, Sheffield Cancer Centre, University of Sheffield, Sheffield, United Kingdom
| | - Ulrika Warpman Berglund
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
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13
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Martínez-Arribas B, Requena CE, Pérez-Moreno G, Ruíz-Pérez LM, Vidal AE, González-Pacanowska D. DCTPP1 prevents a mutator phenotype through the modulation of dCTP, dTTP and dUTP pools. Cell Mol Life Sci 2020; 77:1645-1660. [PMID: 31377845 PMCID: PMC7162842 DOI: 10.1007/s00018-019-03250-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/05/2019] [Accepted: 07/23/2019] [Indexed: 12/02/2022]
Abstract
To maintain dNTP pool homeostasis and preserve genetic integrity of nuclear and mitochondrial genomes, the synthesis and degradation of DNA precursors must be precisely regulated. Human all-alpha dCTP pyrophosphatase 1 (DCTPP1) is a dNTP pyrophosphatase with high affinity for dCTP and 5'-modified dCTP derivatives, but its contribution to overall nucleotide metabolism is controversial. Here, we identify a central role for DCTPP1 in the homeostasis of dCTP, dTTP and dUTP. Nucleotide pools and the dUTP/dTTP ratio are severely altered in DCTPP1-deficient cells, which exhibit an accumulation of uracil in genomic DNA, the activation of the DNA damage response and both a mitochondrial and nuclear hypermutator phenotype. Notably, DNA damage can be reverted by incubation with thymidine, dUTPase overexpression or uracil-DNA glycosylase suppression. Moreover, DCTPP1-deficient cells are highly sensitive to down-regulation of nucleoside salvage. Our data indicate that DCTPP1 is crucially involved in the provision of dCMP for thymidylate biosynthesis, introducing a new player in the regulation of pyrimidine dNTP levels and the maintenance of genomic integrity.
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Affiliation(s)
- Blanca Martínez-Arribas
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
| | - Cristina E Requena
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Guiomar Pérez-Moreno
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
| | - Luis M Ruíz-Pérez
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
| | - Antonio E Vidal
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
| | - Dolores González-Pacanowska
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain.
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14
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Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, O'Meara MJ, Guo JZ, Swaney DL, Tummino TA, Hüttenhain R, Kaake RM, Richards AL, Tutuncuoglu B, Foussard H, Batra J, Haas K, Modak M, Kim M, Haas P, Polacco BJ, Braberg H, Fabius JM, Eckhardt M, Soucheray M, Bennett MJ, Cakir M, McGregor MJ, Li Q, Naing ZZC, Zhou Y, Peng S, Kirby IT, Melnyk JE, Chorba JS, Lou K, Dai SA, Shen W, Shi Y, Zhang Z, Barrio-Hernandez I, Memon D, Hernandez-Armenta C, Mathy CJP, Perica T, Pilla KB, Ganesan SJ, Saltzberg DJ, Ramachandran R, Liu X, Rosenthal SB, Calviello L, Venkataramanan S, Lin Y, Wankowicz SA, Bohn M, Trenker R, Young JM, Cavero D, Hiatt J, Roth T, Rathore U, Subramanian A, Noack J, Hubert M, Roesch F, Vallet T, Meyer B, White KM, Miorin L, Agard D, Emerman M, Ruggero D, García-Sastre A, Jura N, von Zastrow M, Taunton J, Schwartz O, Vignuzzi M, d'Enfert C, Mukherjee S, Jacobson M, Malik HS, Fujimori DG, Ideker T, Craik CS, Floor S, Fraser JS, Gross J, Sali A, Kortemme T, Beltrao P, Shokat K, Shoichet BK, Krogan NJ. A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.03.22.002386. [PMID: 32511329 PMCID: PMC7239059 DOI: 10.1101/2020.03.22.002386] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An outbreak of the novel coronavirus SARS-CoV-2, the causative agent of COVID-19 respiratory disease, has infected over 290,000 people since the end of 2019, killed over 12,000, and caused worldwide social and economic disruption 1,2 . There are currently no antiviral drugs with proven efficacy nor are there vaccines for its prevention. Unfortunately, the scientific community has little knowledge of the molecular details of SARS-CoV-2 infection. To illuminate this, we cloned, tagged and expressed 26 of the 29 viral proteins in human cells and identified the human proteins physically associated with each using affinity-purification mass spectrometry (AP-MS), which identified 332 high confidence SARS-CoV-2-human protein-protein interactions (PPIs). Among these, we identify 66 druggable human proteins or host factors targeted by 69 existing FDA-approved drugs, drugs in clinical trials and/or preclinical compounds, that we are currently evaluating for efficacy in live SARS-CoV-2 infection assays. The identification of host dependency factors mediating virus infection may provide key insights into effective molecular targets for developing broadly acting antiviral therapeutics against SARS-CoV-2 and other deadly coronavirus strains.
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Affiliation(s)
- David E Gordon
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Gwendolyn M Jang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Mehdi Bouhaddou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jiewei Xu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Kirsten Obernier
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Matthew J O'Meara
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jeffrey Z Guo
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Danielle L Swaney
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Tia A Tummino
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Ruth Hüttenhain
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Robyn M Kaake
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Alicia L Richards
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Beril Tutuncuoglu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Helene Foussard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jyoti Batra
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Kelsey Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Maya Modak
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Minkyu Kim
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Paige Haas
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Benjamin J Polacco
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Hannes Braberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Jacqueline M Fabius
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Manon Eckhardt
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Margaret Soucheray
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Melanie J Bennett
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Merve Cakir
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Michael J McGregor
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Qiongyu Li
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Zun Zar Chi Naing
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Yuan Zhou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Shiming Peng
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Ilsa T Kirby
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - James E Melnyk
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - John S Chorba
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Kevin Lou
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Shizhong A Dai
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Wenqi Shen
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Ying Shi
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Ziyang Zhang
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Inigo Barrio-Hernandez
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Danish Memon
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Claudia Hernandez-Armenta
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Christopher J P Mathy
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco.,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA
| | - Tina Perica
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Kala B Pilla
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Sai J Ganesan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Daniel J Saltzberg
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Rakesh Ramachandran
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Xi Liu
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Sara B Rosenthal
- Center for Computational Biology and Bioinformatics, Department of Medicine, University of California San Diego
| | - Lorenzo Calviello
- Department of Cell and Tissue Biology, University of California, San Francisco
| | | | - Yizhu Lin
- Department of Cell and Tissue Biology, University of California, San Francisco
| | - Stephanie A Wankowicz
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco.,Biophysics Graduate Program, University of California, San Francisco
| | - Markus Bohn
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Raphael Trenker
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Janet M Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center
| | - Devin Cavero
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Joe Hiatt
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Theo Roth
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ujjwal Rathore
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA
| | - Advait Subramanian
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Julia Noack
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Mathieu Hubert
- Virus and Immunity Unit, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Ferdinand Roesch
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Björn Meyer
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Kris M White
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Lisa Miorin
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - David Agard
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,Biochemistry & Biophysics and Quantitative Biosciences Institute UCSF 600 16th St San Francisco, CA 94143
| | - Michael Emerman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98103
| | - Davide Ruggero
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Adolfo García-Sastre
- Department for Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Natalia Jura
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Mark von Zastrow
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Psychiatry, San Francisco, CA, 94158, USA
| | - Jack Taunton
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
| | - Olivier Schwartz
- Virus and Immunity Unit, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, CNRS UMR 3569, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Christophe d'Enfert
- Direction Scientifique, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
| | - Shaeri Mukherjee
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,George William Hooper Foundation, Department of Microbiology and Immunology, UC San Francisco
| | - Matt Jacobson
- Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Harmit S Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center
| | - Danica G Fujimori
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Trey Ideker
- Division of Genetics, Department of Medicine, University of California San Diego
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA
| | - Stephen Floor
- Department of Cell and Tissue Biology, University of California, San Francisco.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA
| | - James S Fraser
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - John Gross
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Andrej Sali
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco
| | - Tanja Kortemme
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco.,The UC Berkeley-UCSF Graduate Program in Bioengineering, University of California San Francisco, San Francisco, CA, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA
| | - Pedro Beltrao
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kevan Shokat
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA.,Howard Hughes Medical Institute
| | - Brian K Shoichet
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco
| | - Nevan J Krogan
- QBI COVID-19 Research Group (QCRG), San Francisco, CA, 94158, USA.,University of California San Francisco, Quantitative Biosciences Institute (QBI), San Francisco, CA, 94158, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,University of California San Francisco, Department of Cellular and Molecular Pharmacology, San Francisco, CA, 94158, USA
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15
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Scaletti E, Claesson M, Helleday T, Jemth AS, Stenmark P. The First Structure of an Active Mammalian dCTPase and its Complexes With Substrate Analogs and Products. J Mol Biol 2020; 432:1126-1142. [PMID: 31954130 DOI: 10.1016/j.jmb.2020.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/30/2019] [Accepted: 01/03/2020] [Indexed: 11/26/2022]
Abstract
Precise regulation of dNTPs within the cellular nucleotide pool is essential for high accuracy of DNA replication and is critical for retaining the genomic integrity. Recently, human dCTPase (deoxycytidine triphosphatase), also known as DCTPP1 (human all-alpha dCTP pyrophosphatase 1), has been revealed to be a key player in the balance of pyrimidine nucleotide concentrations within cells, with DCTPP1 deficiency causing DNA damage and genetic instability in both chromosomal and mitochondrial DNA. DCTPP1 also exhibits an additional "house cleaning" function as it has been shown to be highly active against modified cytidine triphosphates, such as 5-methyl-dCTP, which, if incorrectly incorporated into DNA can introduce undesirable epigenetic marking. To date, structural studies of mammalian dCTPase have been limited to inactive constructs, which do not provide information regarding the catalytic mechanism of this important enzyme. We present here the first structures of an active mammalian dCTPase from M. musculus in complex with the nonhydrolyzable substrate analog dCMPNPP and the products 5-Me-dCMP and dCMP. These structures provide clear insights into substrate binding and catalysis and clearly elucidate why previous structures of mammalian dCTPase were catalytically inactive. The overall structure of M. musculus dCTPase is highly similar to enzymes from the all-alpha NTP phosphohydrolase superfamily. Comparison of M. musculus dCTPase with homologs from a diverse range of mammals, including humans, shows that the residues, which contribute to substrate recognition, are entirely conserved, further supporting the importance of this enzyme in the protection of genomic integrity in mammalian cells.
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Affiliation(s)
- Emma Scaletti
- Department of Experimental Medical Science, Lund University, Lund, 221 00, Sweden; Department of Biochemistry and Biophysics, Stockholm University, Stockholm, S-106 91, Sweden
| | - Magnus Claesson
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, S-106 91, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, S-171 76, Sweden; Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
| | - Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, S-171 76, Sweden.
| | - Pål Stenmark
- Department of Experimental Medical Science, Lund University, Lund, 221 00, Sweden; Department of Biochemistry and Biophysics, Stockholm University, Stockholm, S-106 91, Sweden.
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16
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Friese A, Kapoor S, Schneidewind T, Vidadala SR, Sardana J, Brause A, Förster T, Bischoff M, Wagner J, Janning P, Ziegler S, Waldmann H. Chemical Genetics Reveals a Role of dCTP Pyrophosphatase 1 in Wnt Signaling. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905977] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alexandra Friese
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Shobhna Kapoor
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Present address: Department of Chemistry Indian Institute of Technology Bombay Powai Mumbai- 400076 Maharashtra India
| | - Tabea Schneidewind
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Srinivasa Rao Vidadala
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Present address: Syngene International Limited Bengaluru Karnataka 560099 India
| | - Juhi Sardana
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Alexandra Brause
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Tim Förster
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Matthias Bischoff
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Jessica Wagner
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technische Universität Dortmund Otto-Hahn Strasse 6 44227 Dortmund Germany
| | - Petra Janning
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Slava Ziegler
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Herbert Waldmann
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technische Universität Dortmund Otto-Hahn Strasse 6 44227 Dortmund Germany
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17
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Friese A, Kapoor S, Schneidewind T, Vidadala SR, Sardana J, Brause A, Förster T, Bischoff M, Wagner J, Janning P, Ziegler S, Waldmann H. Chemical Genetics Reveals a Role of dCTP Pyrophosphatase 1 in Wnt Signaling. Angew Chem Int Ed Engl 2019; 58:13009-13013. [DOI: 10.1002/anie.201905977] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Alexandra Friese
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Shobhna Kapoor
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Present address: Department of Chemistry Indian Institute of Technology Bombay Powai Mumbai- 400076 Maharashtra India
| | - Tabea Schneidewind
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Srinivasa Rao Vidadala
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Present address: Syngene International Limited Bengaluru Karnataka 560099 India
| | - Juhi Sardana
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Alexandra Brause
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Tim Förster
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Matthias Bischoff
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Jessica Wagner
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technische Universität Dortmund Otto-Hahn Strasse 6 44227 Dortmund Germany
| | - Petra Janning
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Slava Ziegler
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Herbert Waldmann
- Department of Chemical Biology Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
- Faculty of Chemistry and Chemical Biology Technische Universität Dortmund Otto-Hahn Strasse 6 44227 Dortmund Germany
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18
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Tsesmetzis N, Paulin CBJ, Rudd SG, Herold N. Nucleobase and Nucleoside Analogues: Resistance and Re-Sensitisation at the Level of Pharmacokinetics, Pharmacodynamics and Metabolism. Cancers (Basel) 2018; 10:cancers10070240. [PMID: 30041457 PMCID: PMC6071274 DOI: 10.3390/cancers10070240] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 02/07/2023] Open
Abstract
Antimetabolites, in particular nucleobase and nucleoside analogues, are cytotoxic drugs that, starting from the small field of paediatric oncology, in combination with other chemotherapeutics, have revolutionised clinical oncology and transformed cancer into a curable disease. However, even though combination chemotherapy, together with radiation, surgery and immunotherapy, can nowadays cure almost all types of cancer, we still fail to achieve this for a substantial proportion of patients. The understanding of differences in metabolism, pharmacokinetics, pharmacodynamics, and tumour biology between patients that can be cured and patients that cannot, builds the scientific basis for rational therapy improvements. Here, we summarise current knowledge of how tumour-specific and patient-specific factors can dictate resistance to nucleobase/nucleoside analogues, and which strategies of re-sensitisation exist. We revisit well-established hurdles to treatment efficacy, like the blood-brain barrier and reduced deoxycytidine kinase activity, but will also discuss the role of novel resistance factors, such as SAMHD1. A comprehensive appreciation of the complex mechanisms that underpin the failure of chemotherapy will hopefully inform future strategies of personalised medicine.
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Affiliation(s)
- Nikolaos Tsesmetzis
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 171 77 Stockholm, Sweden.
| | - Cynthia B J Paulin
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden.
| | - Sean G Rudd
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, 171 65 Stockholm, Sweden.
| | - Nikolas Herold
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, 171 77 Stockholm, Sweden.
- Paediatric Oncology, Theme of Children's and Women's Health, Karolinska University Hospital Solna, 171 76 Stockholm, Sweden.
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19
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Abstract
Small molecules have extensive untapped potential to benefit society, but access to this potential is too often restricted by limitations inherent to the customized approach currently used to synthesize this class of chemical matter. In contrast, the "building block approach", i.e., generalized iterative assembly of interchangeable parts, has now proven to be a highly efficient and flexible way to construct things ranging all the way from skyscrapers to macromolecules to artificial intelligence algorithms. The structural redundancy found in many small molecules suggests that they possess a similar capacity for generalized building block-based construction. It is also encouraging that many customized iterative synthesis methods have been developed that improve access to specific classes of small molecules. There has also been substantial recent progress toward the iterative assembly of many different types of small molecules, including complex natural products, pharmaceuticals, biological probes, and materials, using common building blocks and coupling chemistry. Collectively, these advances suggest that a generalized building block approach for small molecule synthesis may be within reach.
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Affiliation(s)
- Jonathan W Lehmann
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Daniel J Blair
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Martin D Burke
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA and Carle-Illinois College of Medicine, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA
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20
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Tetrahydrobenzothiophene carboxamides: Beyond the kinase domain and into the fatty acid realm. Bioorg Med Chem Lett 2017; 27:4462-4466. [DOI: 10.1016/j.bmcl.2017.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 11/21/2022]
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21
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Diverse heterocyclic scaffolds as dCTP pyrophosphatase 1 inhibitors. Part 1: Triazoles, triazolopyrimidines, triazinoindoles, quinoline hydrazones and arylpiperazines. Bioorg Med Chem Lett 2017; 27:3897-3904. [PMID: 28687206 DOI: 10.1016/j.bmcl.2017.06.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 06/12/2017] [Accepted: 06/14/2017] [Indexed: 10/19/2022]
Abstract
A high-throughput screening campaign using a commercial compound library (ChemBridge DiverSET) revealed diverse chemotypes as inhibitors of the human dCTP pyrophosphatase 1 (dCTPase). Triazole, triazolopyrimidine, triazinoindole, quinoline hydrazone and arylpiperazine hits were clustered, confirmed by IC50 determinations, and their preliminary structure-activity-relationships (SAR) and ligand efficiency scores are discussed in this letter.
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22
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The versatility of boron in biological target engagement. Nat Chem 2017; 9:731-742. [DOI: 10.1038/nchem.2814] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/12/2017] [Indexed: 12/20/2022]
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23
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Diverse heterocyclic scaffolds as dCTP pyrophosphatase 1 inhibitors. Part 2: Pyridone- and pyrimidinone-derived systems. Bioorg Med Chem Lett 2017; 27:3219-3225. [PMID: 28655422 DOI: 10.1016/j.bmcl.2017.06.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 06/12/2017] [Accepted: 06/14/2017] [Indexed: 12/29/2022]
Abstract
Two screening campaigns using commercial (Chembridge DiverSET) and proprietary (Chemical Biology Consortium Sweden, CBCS) compound libraries, revealed a number of pyridone- and pyrimidinone-derived systems as inhibitors of the human dCTP pyrophosphatase 1 (dCTPase). In this letter, we present their preliminary structure-activity-relationships (SAR) and ligand efficiency scores (LE and LLE).
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24
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Llona-Minguez S, Höglund A, Ghassemian A, Desroses M, Calderón-Montaño JM, Burgos Morón E, Valerie NCK, Wiita E, Almlöf I, Koolmeister T, Mateus A, Cazares-Körner C, Sanjiv K, Homan E, Loseva O, Baranczewski P, Darabi M, Mehdizadeh A, Fayezi S, Jemth AS, Warpman Berglund U, Sigmundsson K, Lundbäck T, Jenmalm Jensen A, Artursson P, Scobie M, Helleday T. Piperazin-1-ylpyridazine Derivatives Are a Novel Class of Human dCTP Pyrophosphatase 1 Inhibitors. J Med Chem 2017; 60:4279-4292. [DOI: 10.1021/acs.jmedchem.7b00182] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sabin Llona-Minguez
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Andreas Höglund
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Artin Ghassemian
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Matthieu Desroses
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - José Manuel Calderón-Montaño
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Estefanía Burgos Morón
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Nicholas C. K. Valerie
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Elisee Wiita
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Ingrid Almlöf
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Tobias Koolmeister
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - André Mateus
- Uppsala
University Drug Optimization and Pharmaceutical Profiling Platform
(UDOPP), Department of Pharmacy, Science for Life Laboratory, Uppsala University, Uppsala 752 37, Sweden
| | - Cindy Cazares-Körner
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Kumar Sanjiv
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Evert Homan
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Olga Loseva
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Pawel Baranczewski
- Uppsala
University Drug Optimization and Pharmaceutical Profiling Platform
(UDOPP), Department of Pharmacy, Science for Life Laboratory, Uppsala University, Uppsala 752 37, Sweden
| | - Masoud Darabi
- Department
of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz 5165665931, Iran
| | - Amir Mehdizadeh
- Department
of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz 5165665931, Iran
| | - Shabnam Fayezi
- Department
of Biology and Anatomical Sciences, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 1983969411, Iran
| | - Ann-Sofie Jemth
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Ulrika Warpman Berglund
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Kristmundur Sigmundsson
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
- Chemical
Biology Consortium Sweden, Science for Life Laboratory, Division of
Translational Medicine and Chemical Biology, Department of Medical
Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Thomas Lundbäck
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
- Chemical
Biology Consortium Sweden, Science for Life Laboratory, Division of
Translational Medicine and Chemical Biology, Department of Medical
Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Annika Jenmalm Jensen
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
- Chemical
Biology Consortium Sweden, Science for Life Laboratory, Division of
Translational Medicine and Chemical Biology, Department of Medical
Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Per Artursson
- Uppsala
University Drug Optimization and Pharmaceutical Profiling Platform
(UDOPP), Department of Pharmacy, Science for Life Laboratory, Uppsala University, Uppsala 752 37, Sweden
| | - Martin Scobie
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
| | - Thomas Helleday
- Division
of Translational Medicine and Chemical Biology, Science for Life Laboratory,
Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 65, Sweden
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25
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Menteşe E, Bektaş H, Sokmen BB, Emirik M, Çakır D, Kahveci B. Synthesis and molecular docking study of some 5,6-dichloro-2-cyclopropyl-1H-benzimidazole derivatives bearing triazole, oxadiazole, and imine functionalities as potent inhibitors of urease. Bioorg Med Chem Lett 2017; 27:3014-3018. [PMID: 28526368 DOI: 10.1016/j.bmcl.2017.05.019] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 12/17/2022]
Abstract
A new series of benzimidazole compounds including hydrazinecarbothioamide, 1,2,4-triazole, 1,3,4-oxadiazole and imine function were synthesized starting from 5,6-dichloro-2-cyclopropyl-1H-benzimidazole. All of the benzimidazole derivatives exhibited good urease inhibitor activity. Compound 6a proved to be the most potent showing an enzyme inhibitory activity with an IC50=0.06µM. Molecular docking studies were also conducted on enzyme extracted from Jack bean urease to identify the binding mode of the newly synthesized compounds.
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Affiliation(s)
- Emre Menteşe
- Department of Chemistry, Art and Science Faculty, Recep Tayyip Erdogan University, Rize, Turkey.
| | - Hakan Bektaş
- Department of Chemistry, Faculty of Arts and Sciences, Giresun University, 28049 Giresun, Turkey
| | - Bahar Bilgin Sokmen
- Department of Chemistry, Faculty of Arts and Sciences, Giresun University, 28049 Giresun, Turkey
| | - Mustafa Emirik
- Department of Chemistry, Art and Science Faculty, Recep Tayyip Erdogan University, Rize, Turkey
| | - Demet Çakır
- Department of Chemistry, Faculty of Arts and Sciences, Giresun University, 28049 Giresun, Turkey
| | - Bahittin Kahveci
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Karadeniz Technical University, Trabzon, Turkey
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26
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Human pyrimidine nucleotide biosynthesis as a target for antiviral chemotherapy. Curr Opin Biotechnol 2017; 48:127-134. [PMID: 28458037 DOI: 10.1016/j.copbio.2017.03.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 03/10/2017] [Indexed: 01/03/2023]
Abstract
The development of broad-spectrum, host-acting antiviral therapies remains an important but elusive goal in anti-infective drug discovery. To replicate efficiently, viruses not only depend on their hosts for an adequate supply of pyrimidine nucleotides, but also up-regulate pyrimidine nucleotide biosynthesis in infected cells. In this review, we outline our understanding of mammalian de novo and salvage metabolic pathways for pyrimidine nucleotide biosynthesis. The available spectrum of experimental and FDA-approved drugs that modulate individual steps in these metabolic pathways is also summarized. The logic of a host-acting combination antiviral therapy comprised of inhibitors of dihydroorotate dehydrogenase and uridine/cytidine kinase is discussed.
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27
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Llona-Minguez S, Höglund A, Wiita E, Almlöf I, Mateus A, Calderón-Montaño JM, Cazares-Körner C, Homan E, Loseva O, Baranczewski P, Jemth AS, Häggblad M, Martens U, Lundgren B, Artursson P, Lundbäck T, Jenmalm Jensen A, Warpman Berglund U, Scobie M, Helleday T. Identification of Triazolothiadiazoles as Potent Inhibitors of the dCTP Pyrophosphatase 1. J Med Chem 2017; 60:2148-2154. [PMID: 28145708 DOI: 10.1021/acs.jmedchem.6b01786] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dCTP pyrophosphatase 1 (dCTPase) is involved in the regulation of the cellular dNTP pool and has been linked to cancer progression. Here we report on the discovery of a series of 3,6-disubstituted triazolothiadiazoles as potent dCTPase inhibitors. Compounds 16 and 18 display good correlation between enzymatic inhibition and target engagement, together with efficacy in a cellular synergy model, deeming them as a promising starting point for hit-to-lead development.
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Affiliation(s)
- Sabin Llona-Minguez
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institutet , 17121 Stockholm, Sweden
| | - Andreas Höglund
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institutet , 17121 Stockholm, Sweden
| | - Elisee Wiita
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institutet , 17121 Stockholm, Sweden
| | - Ingrid Almlöf
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institutet , 17121 Stockholm, Sweden
| | - André Mateus
- Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Science for Life Laboratory, Uppsala University , 75123 Uppsala, Sweden
| | - José Manuel Calderón-Montaño
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institutet , 17121 Stockholm, Sweden
| | - Cindy Cazares-Körner
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institutet , 17121 Stockholm, Sweden
| | - Evert Homan
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institutet , 17121 Stockholm, Sweden
| | - Olga Loseva
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institutet , 17121 Stockholm, Sweden
| | - Pawel Baranczewski
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institutet , 17121 Stockholm, Sweden.,Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Science for Life Laboratory, Uppsala University , 75123 Uppsala, Sweden
| | - Ann-Sofie Jemth
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institutet , 17121 Stockholm, Sweden
| | - Maria Häggblad
- RNAi Cell Screening Facility, Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University , S-10691 Stockholm, Sweden
| | - Ulf Martens
- RNAi Cell Screening Facility, Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University , S-10691 Stockholm, Sweden
| | - Bo Lundgren
- RNAi Cell Screening Facility, Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University , S-10691 Stockholm, Sweden
| | - Per Artursson
- Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP), Department of Pharmacy, Science for Life Laboratory, Uppsala University , 75123 Uppsala, Sweden
| | - Thomas Lundbäck
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institutet , 17121 Stockholm, Sweden.,Chemical Biology Consortium Sweden, and Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institutet, 17121 Stockholm, Sweden
| | - Annika Jenmalm Jensen
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institutet , 17121 Stockholm, Sweden.,Chemical Biology Consortium Sweden, and Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institutet, 17121 Stockholm, Sweden
| | - Ulrika Warpman Berglund
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institutet , 17121 Stockholm, Sweden
| | - Martin Scobie
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institutet , 17121 Stockholm, Sweden
| | - Thomas Helleday
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Karolinska Institutet , 17121 Stockholm, Sweden
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28
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Llona-Minguez S, Throup A, Steiner E, Lightowler M, Van der Haegen S, Homan E, Eriksson L, Stenmark P, Jenmalm-Jensen A, Helleday T. Novel spirocyclic systems via multicomponent aza-Diels–Alder reaction. Org Biomol Chem 2017; 15:7758-7764. [DOI: 10.1039/c7ob02069d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we present a two-step diastereoselective methodology building on a multicomponent aza-Diels–Alder reaction.
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29
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Llona-Minguez S, Ghassemian A, Baranczewski P, Desroses M, Koolmeister T, Artursson P, Scobie M, Helleday T. Structure–metabolism-relationships in the microsomal clearance of piperazin-1-ylpyridazines. MEDCHEMCOMM 2017; 8:1553-1560. [DOI: 10.1039/c7md00230k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/20/2017] [Indexed: 11/21/2022]
Abstract
In this study, we provide insight into the metabolic profile of a series of piperazin-1-ylpyridazines suffering from rapid in vitro intrinsic clearance in a metabolic stability assay using liver microsomes.
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Affiliation(s)
- Sabin Llona-Minguez
- Division of Translational Medicine and Chemical Biology
- Science for Life Laboratory
- Department of Medical Biochemistry and Biophysics
- Karolinska Institutet
- Stockholm
| | - Artin Ghassemian
- Division of Translational Medicine and Chemical Biology
- Science for Life Laboratory
- Department of Medical Biochemistry and Biophysics
- Karolinska Institutet
- Stockholm
| | - Pawel Baranczewski
- Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP)
- Science for Life Laboratory
- Department of Pharmacy
- Uppsala University
- Uppsala
| | - Matthieu Desroses
- Division of Translational Medicine and Chemical Biology
- Science for Life Laboratory
- Department of Medical Biochemistry and Biophysics
- Karolinska Institutet
- Stockholm
| | - Tobias Koolmeister
- Division of Translational Medicine and Chemical Biology
- Science for Life Laboratory
- Department of Medical Biochemistry and Biophysics
- Karolinska Institutet
- Stockholm
| | - Per Artursson
- Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP)
- Science for Life Laboratory
- Department of Pharmacy
- Uppsala University
- Uppsala
| | - Martin Scobie
- Division of Translational Medicine and Chemical Biology
- Science for Life Laboratory
- Department of Medical Biochemistry and Biophysics
- Karolinska Institutet
- Stockholm
| | - Thomas Helleday
- Division of Translational Medicine and Chemical Biology
- Science for Life Laboratory
- Department of Medical Biochemistry and Biophysics
- Karolinska Institutet
- Stockholm
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30
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Xia LL, Tang YB, Song FF, Xu L, Ji P, Wang SJ, Zhu JM, Zhang Y, Zhao GP, Wang Y, Liu TT. DCTPP1 attenuates the sensitivity of human gastric cancer cells to 5-fluorouracil by up-regulating MDR1 expression epigenetically. Oncotarget 2016; 7:68623-68637. [PMID: 27612427 PMCID: PMC5356578 DOI: 10.18632/oncotarget.11864] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 08/24/2016] [Indexed: 01/08/2023] Open
Abstract
Gastric cancer (GC) is among the most malignant cancers with high incidence and poor prognoses worldwide as well as in China. dCTP pyrophosphatase 1 (DCTPP1) is overexpressed in GC with a poor prognosis. Given chemotherapeutic drugs share similar structures with pyrimidine nucleotides, the role of DCTPP1 in affecting the drug sensitivity in GC remains unclear and is worthy of investigation. In the present study, we reported that DCTPP1-knockdown GC cell line BGC-823 exhibited more sensitivity to 5-fluorouracil (5-FU), demonstrated by the retardation of cell proliferation, the increase in cell apoptosis, cell cycle arrest at S phase and more DNA damages. Multidrug resistance 1 (MDR1) expression was unexpectedly down-regulated in DCTPP1-knockdown BGC-823 cells together with more intracellular 5-FU accumulation. This was in large achieved by the elevated methylation in promoter region of MDR1 gene. The intracellular 5-methyl-dCTP level increased in DCTPP1-knockdown BGC-823 cells as well. More significantly, the strong correlation of DCTPP1 and MDR1 expression was detectable in clinical GC samples. Our results thus imply a novel mechanism of chemoresistance mediated by the overexpression of DCTPP1 in GC. It is achieved partially through decreasing the concentration of intracellular 5-methyl-dCTP, which in turn results in promoter hypomethylation and hyper-expression of drug resistant gene MDR1. Our study suggests DCTPP1 as a potential indicative biomarker for the predication of chemoresistance in GC.
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Affiliation(s)
- Li-liang Xia
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Ya-bin Tang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Department of Pharmacology and Chemical Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Fei-fei Song
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Department of Pharmacology and Chemical Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ling Xu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Department of Pharmacology and Chemical Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ping Ji
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Department of Pharmacology and Chemical Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Shu-jun Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Department of Pharmacology and Chemical Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ji-min Zhu
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yong Zhang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Department of Pharmacology and Chemical Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Guo-ping Zhao
- State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Ying Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Department of Pharmacology and Chemical Biology, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Tao-tao Liu
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai, China
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31
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Abstract
Artificially modified nucleotides, in the form of nucleoside analogues, are widely used in the treatment of cancers and various other diseases, and have become important tools in the laboratory to characterise DNA repair pathways. In contrast, the role of endogenously occurring nucleotide modifications in genome stability is little understood. This is despite the demonstration over three decades ago that the cellular DNA precursor pool is orders of magnitude more susceptible to modification than the DNA molecule itself. More recently, underscoring the importance of this topic, oxidation of the cellular nucleotide pool achieved through targeting the sanitation enzyme MTH1, appears to be a promising anti-cancer strategy. This article reviews our current understanding of modified DNA precursors in genome stability, with a particular focus upon oxidised nucleotides, and outlines some important outstanding questions.
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Affiliation(s)
- Sean G Rudd
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
| | - Nicholas C K Valerie
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
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32
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The nucleotidohydrolases DCTPP1 and dUTPase are involved in the cellular response to decitabine. Biochem J 2016; 473:2635-43. [PMID: 27325794 DOI: 10.1042/bcj20160302] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/17/2016] [Indexed: 02/03/2023]
Abstract
Decitabine (5-aza-2'-deoxycytidine, aza-dCyd) is an anti-cancer drug used clinically for the treatment of myelodysplastic syndromes and acute myeloid leukaemia that can act as a DNA-demethylating or genotoxic agent in a dose-dependent manner. On the other hand, DCTPP1 (dCTP pyrophosphatase 1) and dUTPase are two 'house-cleaning' nucleotidohydrolases involved in the elimination of non-canonical nucleotides. In the present study, we show that exposure of HeLa cells to decitabine up-regulates the expression of several pyrimidine metabolic enzymes including DCTPP1, dUTPase, dCMP deaminase and thymidylate synthase, thus suggesting their contribution to the cellular response to this anti-cancer nucleoside. We present several lines of evidence supporting that, in addition to the formation of aza-dCTP (5-aza-2'-deoxycytidine-5'-triphosphate), an alternative cytotoxic mechanism for decitabine may involve the formation of aza-dUMP, a potential thymidylate synthase inhibitor. Indeed, dUTPase or DCTPP1 down-regulation enhanced the cytotoxic effect of decitabine producing an accumulation of nucleoside triphosphates containing uracil as well as uracil misincorporation and double-strand breaks in genomic DNA. Moreover, DCTPP1 hydrolyses the triphosphate form of decitabine with similar kinetic efficiency to its natural substrate dCTP and prevents decitabine-induced global DNA demethylation. The data suggest that the nucleotidohydrolases DCTPP1 and dUTPase are factors involved in the mode of action of decitabine with potential value as enzymatic targets to improve decitabine-based chemotherapy.
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33
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R. Shah N, Vidilaseris K, Xhaard H, Goldman A. Integral membrane pyrophosphatases: a novel drug target for human pathogens? AIMS BIOPHYSICS 2016. [DOI: 10.3934/biophy.2016.1.171] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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